Merge pull request #40 from uclahs-cds/sfitz-update-input

Standardize input structure and upgrade from release candidate
uclahs-cds · Mar 13, 2024 · 6ef99eb · 6ef99eb
2 parents 9b60523 + 42a8ca3
commit 6ef99eb
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Showing 9 changed files with 72 additions and 58 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ### Changed
 
+## [1.0.0] - 2024-03-12
+### Changed
+- Standardized input structure
+
 ## [1.0.0-rc.1] - 2024-03-08
 ### Added
 - Add `schema.yaml`

diff --git a/config/custom_schema_types.config b/config/custom_schema_types.config
@@ -1,5 +1,8 @@
 custom_schema_types {
     allowed_input_types = [
+        'BAM'
+    ]
+    allowed_bam_types = [
         'normal',
         'tumor'
     ]
@@ -55,7 +58,7 @@ custom_schema_types {
     }
 
     types = [
-        'BAMEntryList': custom_schema_types.check_list_of_namespace,
+        'MapList': custom_schema_types.check_list_of_namespace,
         'ResourceUpdateNamespace': custom_schema_types.check_resource_update_namespace,
         'ResourceUpdateList': custom_schema_types.check_resource_update_list
     ]

diff --git a/config/methods.config b/config/methods.config
@@ -7,7 +7,7 @@ includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/retry/retr
 methods {
     get_ids_from_bams = {
         params.samples_to_process = [] as Set
-        params.input.each { k, v ->
+        params.input['BAM'].each { k, v ->
             v.each { sampleMap ->
                 def bam_path = sampleMap['path']
                 def bam_header = bam_parser.parse_bam_header(bam_path)

diff --git a/config/schema.yaml b/config/schema.yaml
@@ -107,31 +107,36 @@ input:
   required: true
   help: 'Input to process'
   elements:
-    normal:
-      type: 'BAMEntryList'
-      required: false
-      help: 'Normal sample input specifications'
+    BAM:
+      type: 'InputBAMNamespace'
+      required: true
+      help: 'BAM input specifications'
       elements:
-        path:
-          type: 'Path'
-          mode: 'r'
-          required: true
-          help: 'Absolute path to normal sample BAM files'
-        read_length:
-          type: 'Integer'
+        normal:
+          type: 'MapList'
           required: false
-          help: 'Length of the reads in the BAM file'
-    tumor:
-      type: 'BAMEntryList'
-      required: false
-      help: 'Tumor sample input specifications'
-      elements:
-        path:
-          type: 'Path'
-          mode: 'r'
-          required: true
-          help: 'Absolute path to tumor sample BAM files'
-        read_length:
-          type: 'Integer'
+          help: 'Normal sample input specifications'
+          elements:
+            path:
+              type: 'Path'
+              mode: 'r'
+              required: true
+              help: 'Absolute path to normal sample BAM files'
+            read_length:
+              type: 'Integer'
+              required: false
+              help: 'Length of the reads in the BAM file'
+        tumor:
+          type: 'MapList'
           required: false
-          help: 'Length of the reads in the BAM file'
+          help: 'Tumor sample input specifications'
+          elements:
+            path:
+              type: 'Path'
+              mode: 'r'
+              required: true
+              help: 'Absolute path to tumor sample BAM files'
+            read_length:
+              type: 'Integer'
+              required: false
+              help: 'Length of the reads in the BAM file'
diff --git a/input/example-multiple-samples.yaml b/input/example-multiple-samples.yaml
@@ -2,11 +2,12 @@
 patient_id: 'patient_id'
 dataset_id: 'dataset_id'
 input:
-  normal:
-    - path: /absolute/path/to/normal.bam
-      read_length: length
-  tumor:
-    - path: /absolute/path/to/first.tumor.bam
-      read_length: length
-    - path: /absolute/path/to/second.tumor.bam
-      read_length: length
+  BAM:
+    normal:
+      - path: /absolute/path/to/normal.bam
+        read_length: length
+    tumor:
+      - path: /absolute/path/to/first.tumor.bam
+        read_length: length
+      - path: /absolute/path/to/second.tumor.bam
+        read_length: length
diff --git a/input/example.yaml b/input/example.yaml
@@ -2,9 +2,10 @@
 patient_id: 'patient_id'
 dataset_id: 'dataset_id'
 input:
-  normal:
-    - path: /absolute/path/to/normal.bam
-      read_length: length
-  tumor:
-    - path: /absolute/path/to/tumor.bam
-      read_length: length
+  BAM:
+    normal:
+      - path: /absolute/path/to/normal.bam
+        read_length: length
+    tumor:
+      - path: /absolute/path/to/tumor.bam
+        read_length: length
diff --git a/nextflow.config b/nextflow.config
@@ -3,5 +3,5 @@ manifest {
     name = 'generate-SQC-BAM'
     author = 'Sorel Fitz-Gibbon'
     description = 'Sample level QC for DNA sequencing data'
-    version = '1.0.0-rc.1'
+    version = '1.0.0'
 }
diff --git a/test/yaml/a_mini-multiple-samples.yaml b/test/yaml/a_mini-multiple-samples.yaml
@@ -2,12 +2,12 @@
 patient_id: 'TWGSAMIN000001'
 dataset_id: 'TWGSAMIN'
 input:
-  normal:
-    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
-      read_length: 150
-
-  tumor:
-    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
-      read_length: 150
-    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n1_SMadjust.bam
-      read_length: 150
+  BAM:
+    normal:
+      - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
+        read_length: 150
+    tumor:
+      - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
+        read_length: 150
+      - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n1_SMadjust.bam
+        read_length: 150
diff --git a/test/yaml/a_mini.yaml b/test/yaml/a_mini.yaml
@@ -2,10 +2,10 @@
 patient_id: 'TWGSAMIN000001'
 dataset_id: 'TWGSAMIN'
 input:
-  normal:
-    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
-      read_length: 150
-
-  tumor:
-    - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
-      read_length: 150
+  BAM:
+    normal:
+      - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/HG002.N-n2.bam
+        read_length: 150
+    tumor:
+      - path: /hot/software/pipeline/pipeline-generate-SQC-BAM/Nextflow/development/test-input/S2.T-n2.bam
+        read_length: 150